[BioC] ChiPQC and paired-end data

[Carroll, Thomas]

Hi Ugo,

>To be sure I understand you mean:
>$ samtools view -f 64

That sounds right to get the first in pair.

Cheers,

tom

Thomas Carroll
Head of Bioinformatics
MRC Clinical Sciences Centre, Faculty of Medicine,
Imperial College London,Hammersmith Hospital Campus
Du Cane Road,London,W12 0NN

________________________________________
From: Ugo Borello [ugo.borello at inserm.fr]
Sent: Wednesday, July 30, 2014 3:05 PM
To: Carroll, Thomas; bioconductor at r-project.org
Subject: Re: [BioC] ChiPQC and paired-end data

Thank you Thomas,

> You could use paired-end data with ChIPQC but for now this would require you
> to filter your Bam file for only "first read in pair" in order to avoid double
> counting and biasing the cross-coverage scores plots.
> This should be pretty straightforward to do using samtools view.

To be sure I understand you mean:
$ samtools view -f 64

> To retrieve consensus sets you could take the DBA object from ChIPQCexperiment
> and work from there using the Diffbind package.
>
> dbaobject = ChIPQCexperiment at DBA
Indeed, I finally got my consensus playing with  the Diffbind package. I
needed to understand how to link properly ChIPQC with Diffbind.

Thank you again for your help.

Ugo




> From: "Carroll, Thomas" <thomas.carroll at csc.mrc.ac.uk>
> Date: Mon, 28 Jul 2014 12:16:15 +0000
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Cc: "ugo.borello at inserm.fr" <ugo.borello at inserm.fr>
> Subject: Re: [BioC] ChiPQC and paired-end data
>
> Hi Ugo,
>
> Sorry for the delay in reply. If you include the maintainers in the post then
> I will get a quicker notification.
>
>
> I usually supply blacklists as GRanges objects and this is what i have done
> when using mm9 blacklists myself form Anshul Kudaje's site. ChIPQC expects
> there to be a header when reading from a file.
>
> You could use paired-end data with ChIPQC but for now this would require you
> to filter your Bam file for only "first read in pair" in order to avoid double
> counting and biasing the cross-coverage scores plots.
> This should be pretty straightforward to do using samtools view.
>
> In the future we will include paired-end data analysis for ChIPQC. Not sure
> how Diffbind handles paired end data, perhaps Rory has an idea?
>
>
>
>
> To retrieve consensus sets you could take the DBA object from ChIPQCexperiment
> and work from there using the Diffbind package.
>
> dbaobject = ChIPQCexperiment at DBA
>
>
> Then simply follow DiffBind vignette to select a suitable consensus set.
>
>
> best,
>
> Tom
>
>
> Thomas Carroll
> Head of Bioinformatics
> MRC Clinical Sciences Centre, Faculty of Medicine,
> Imperial College London,Hammersmith Hospital Campus
> Du Cane Road,London,W12 0NN